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Development 140, 3478-3485 (2013) doi:10.1242/dev.097204
© 2013. Published by The Company of Biologists Ltd
The histone H3-K27 demethylase Utx regulates HOX gene
expression in Drosophila in a temporally restricted manner
Ömer Copur and Jürg Müller*
Trimethylation of histone H3 at lysine 27 (H3-K27me3) by Polycomb repressive complex 2 (PRC2) is a key step for transcriptional
repression by the Polycomb system. Demethylation of H3-K27me3 by Utx and/or its paralogs has consequently been proposed to be
important for counteracting Polycomb repression. To study the phenotype of Drosophila mutants that lack H3-K27me3 demethylase
activity, we created UtxΔ, a deletion allele of the single Drosophila Utx gene. UtxΔ homozygotes that contain maternally deposited
wild-type Utx protein develop into adults with normal epidermal morphology but die shortly after hatching. By contrast, UtxΔ
homozygotes that are derived from Utx mutant germ cells and therefore lack both maternal and zygotic Utx protein, die as larvae
and show partial loss of expression of HOX genes in tissues in which these genes are normally active. This phenotype classifies Utx as
a trithorax group regulator. We propose that Utx is needed in the early embryo to prevent inappropriate instalment of long-term
Polycomb repression at HOX genes in cells in which these genes must be kept active. In contrast to PRC2, which is essential for, and
continuously required during, germ cell, embryonic and larval development, Utx therefore appears to have a more limited and specific
function during development. This argues against a continuous interplay between H3-K27me3 methylation and demethylation in the
control of gene transcription in Drosophila. Furthermore, our analyses do not support the recent proposal that Utx would regulate
cell proliferation in Drosophila as Utx mutant cells generated in wild-type animals proliferate like wild-type cells.
Enzymes that add or remove post-translational modifications at
specific amino acid residues of histone proteins have emerged as an
important class of transcriptional regulators. Among these
regulators are the Polycomb group (PcG) proteins, which form
several distinct multiprotein complexes with specific histonemodifying activities (reviewed by Schwartz and Pirrotta, 2008;
Müller and Verrijzer, 2009; Beisel and Paro, 2011; Lanzuolo and
Orlando, 2012; O’Meara and Simon, 2012; Scheuermann et al.,
2012). PcG proteins were first identified through genetic studies in
Drosophila, where they are required for the repression of HOX and
other developmental regulator genes. In particular, Polycomb
complexes are essential for keeping HOX genes inactive in the
progeny of cells in which these genes were initially repressed by
transcriptional regulators that were transiently present in the early
Drosophila embryo. Repression by PcG complexes is therefore
thought to comprise an epigenetic memory mechanism that permits
the heritable propagation of this repression throughout development
(reviewed by Ringrose and Paro, 2004). The discovery that
Polycomb repressive complex 2 (PRC2) is a histone
methyltransferase that specifically methylates lysine 27 of histone
H3 (H3-K27) and that trimethylation of H3-K27 (H3-K27me3) is
present across extended stretches of chromatin at PcG-repressed
genes, has made this modification an attractive candidate for a
chromatin mark that might be inherited through replication and
MPI of Biochemistry, Chromatin and Chromosome Biology, Am Klopferspitz 18,
82152 Martinsried, Germany.
*Author for correspondence ([email protected])
This is an Open Access article distributed under the terms of the Creative Commons Attribution
License (, which permits unrestricted use, distribution
and reproduction in any medium provided that the original work is properly attributed.
Accepted 11 June 2013
mitosis (Cao et al., 2002; Czermin et al., 2002; Kuzmichev et al.,
2002; Müller et al., 2002; Bernstein et al., 2006; Papp and Müller,
2006; Schwartz et al., 2006; Trojer and Reinberg, 2006; Mikkelsen
et al., 2007; Schuettengruber et al., 2009; Hansen et al., 2008;
Margueron et al., 2009; Filion et al., 2010). Recent studies in
Drosophila showed that cells in which wild-type histone H3 has
been replaced by the nonmethylatable mutant H3K27R fail to
maintain Polycomb repression (Pengelly et al., 2013). This provides
strong evidence that methylation of H3-K27 is indeed crucial for
the repression of Polycomb target genes in Drosophila.
Earlier studies identified H3-K27-specific demethylases. In
particular, Utx and the related JmjD3 protein were found to
demethylate H3-K27me3 in vitro and in vivo (Agger et al., 2007; De
Santa et al., 2007; Hong et al., 2007; Lan et al., 2007; Lee et al.,
2007; Swigut and Wysocka, 2007). The discovery of these enzymes
suggested that H3-K27me3 in chromatin might be added and
removed in a dynamic fashion. This challenged the view of H3K27me3 as a stable epigenetic mark that, once installed on an array
of nucleosomes, could only be removed by eviction of the modified
octamer or by dilution due to deposition of unmodified octamers
during DNA replication.
To understand the role of H3-K27me3 demethylation, it is
essential to determine the phenotype of animals that lack H3K27me3 demethylase activity and to investigate how the expression
of PRC2-regulated genes is affected in such animals. Mouse, worm
and flies contain different numbers of H3-K27me3 demethylase
paralogs that are all characterised by a catalytic JmjC domain with
an adjacent zinc-binding domain that is important for substrate
specificity (Sengoku and Yokoyama, 2011; Kim and Song, 2011).
The mouse genome encodes three H3-K27me3 demethylase
family members: the Utx (Kdm6a – Mouse Genome Informatics)
gene on the X chromosome, the Uty gene on the Y chromosome
and JmjD3 (Kdm6b – Mouse Genome Informatics). Recent studies
reported that Utx homozygous mutant female mice die during
KEY WORDS: Polycomb, PcG, Trithorax, trxG, Utx, H3-K27me3
Utx function in Drosophila
Fly strains
The following Drosophila strains were used in this study:
y w;Utx∆/CyO, twi:GAL4, UAS:GFP;
y w;Utx∆ FRT40A/CyO;
y w hs-flp, tubP:GAL4, UAS:nGFP; tubP:GAL80 FRT40A/CyO;
y w hs-flp; ovoD1 FRT40A/CyO, hs:hid;
w; Utx1 FRT40A/CyO, twi:GAL4, UAS:GFP;
w; Df(2L)BSC143/CyO, twi:GAL4, UAS:GFP;
y w hs-flp; hs-nGFP FRT40A;
y w hs-flp; hs-nGFP F2A;
y w; ash122 F2A/TM6C;
y w hs-flp; [Utx∆; hs-nGFP F2A]/SM5^TM6;
w; [Utx∆; ash122 F2A]/SM5^TM6; and
w; FRT40A.
Generation of the UtxΔ allele
The ends-out recombination strategy was used to generate Utx∆ by replacing
the Utx JmjC coding region (Utx503-952) with a miniwhite marker gene
following the strategy described (Gong and Golic, 2003). In brief, for the
Utx disruption construct, 3.5 kb of Utx 3⬘ coding and downstream sequences
(FlyBase 2L:10269938..10273485) and 3.5 kb of 5⬘ coding and upstream
sequences (FlyBase 2L:10275043..10278555) were cloned into pw35
(Gong and Golic, 2003). In this construct, the coding region of Utx503-952
[FlyBase 2L:10273487..10275042 (on the minus strand)] was thus replaced
by the miniwhite gene from pw35; the AGC codon for Ser503 was replaced
with an in-frame TAA termination codon after the His502 codon of Utx.
Analysis of survival into adults
To determine the fraction of animals developing into adults, three
independent batches of 100 first instar larvae of genotype wild type,
Utx∆/Utx∆, Utx∆/Df(2L)BSC143, Utx1/Utx1 and Utx1/Df(2L)BSC143 were
collected, transferred into a vial with food, and larvae were reared at 25°C.
Flies that eclosed from the pupal case were counted.
Western blot analysis
To analyse Utx protein in wild-type or mutant larvae, total extracts from
imaginal discs and CNS tissues of 50 third instar wild-type, Utx∆/Utx∆ or
Utx1/Utx1 larvae were prepared by resuspending the tissues in 100 μl 1×LDS
buffer (Life Technologies), sonication and then heating at 75°C for
5 minutes. The tissue suspension was centrifuged and 20 μl supernatant of
each preparation was run on an 8% SDS polyacrylamide gel. The membrane
was probed with anti-Utx420-633 antibody (Tie et al., 2012) or with anti-Utx1153 antibody (Herz et al., 2010). For the analysis of histone modifications,
total extracts from imaginal discs and CNS tissues were prepared the same
way, using 50 third instar larvae of genotype wild type, Utx∆/Df(2L)BSC143
or Utx1/Df(2L)BSC143. Serial dilutions using 6, 3 and 1.5 μl of each extract
were loaded on a 15% SDS polyacrylamide gel. Membranes were probed
with anti-H3-K27me3 (1:5000) (Peters et al., 2003), anti-H3-K27ac
(1:5000; Active Motif), anti-H3-K4me1 (1:1000; Upstate) or anti-H4
(1:5000; Abcam) antibodies.
Immunostaining of embryos and imaginal discs and preparation
of adult cuticles
Preparation of embryonic cuticles, staining of embryos and larval imaginal
discs and clonal analysis were performed following standard protocols. The
following antibodies were used: anti-H3-K27me3 (1:300) (Peters et al.,
2003), anti-H3-K27ac (1:300; Active Motif), anti-Ubx (1:30) (White and
Wilcox, 1984) and anti-Abd-B (1:100) (Celniker et al., 1990). DNA was
stained with Hoechst.
Zygotic Utx function is dispensable for
morphogenesis but essential for adult viability
To investigate the function of Utx in Drosophila development, we
used a homologous recombination strategy (Gong and Golic, 2003)
to generate Utx∆, a deletion allele that lacks most of the JmjC
catalytic domain and additional portions of the Utx coding region
embryonic development with defects in heart and neural tube
morphogenesis and that males lacking both Utx and Uty show the
same phenotype but that males only lacking Utx develop into
normal and fertile adults (Lee et al., 2012; Shpargel et al., 2012;
Welstead et al., 2012; Wang et al., 2012; Thieme et al., 2013). Uty
thus evidently compensates for the lack of Utx in male Utx mutants
(Shpargel et al., 2012). However, there is currently no evidence that
Uty has H3-K27me3 demethylase activity, even though the catalytic
JmjC domain and the adjacent zinc finger are highly conserved
(Hong et al., 2007; Shpargel et al., 2012). Moreover, in a
differentiation assay in vitro, knock-in male embryonic stem cells
(ESCs) that express full-length but catalytically inactive Utx instead
of the wild-type protein show normal induction of mesodermal
marker genes, whereas knockout cells lacking Utx protein fail to
induce expression of these genes (Wang et al., 2012). Together,
these studies led to the suggestion that the Utx/Uty proteins, but not
their H3-K27me3 demethylase activity, are crucial for normal
embryonic development (Shpargel et al., 2012; Wang et al., 2012).
Jmjd3 mutant mice have been reported to be perinatal lethal (Satoh
et al., 2010). At present, it is unclear whether the H3-K27me3
demethylase activities of JmjD3 and Utx compensate for each other
(Lee et al., 2012; Shpargel et al., 2012; Welstead et al., 2012; Wang
et al., 2012). Studies in tissue culture cell models suggest that Utx
demethylates H3-K27me3 in target gene chromatin through a
mechanism that requires elongating polymerase (Seenundun et al.,
2010), whereas JmjD3 has been implicated to be required for the
release of poised RNA polymerase II into productive transcriptional
elongation (Chen et al., 2012).
C. elegans contains utx-1 and three JmjD3 genes (Vandamme et
al., 2012). utx-1 mutant worms that are derived from heterozygous
mothers and therefore contain maternally deposited wild-type UTX1 protein are viable and show no morphological abnormalities.
However, the mutant progeny from utx-1 homozygotes (i.e. lacking
both zygotic and maternal UTX-1 protein) arrest development at
the late embryonic stage (Vandamme et al., 2012). Intriguingly, this
phenotype can be rescued not only by wild-type but also by a
catalytically inactive UTX-1 protein, suggesting that UTX-1
protein, but not its H3-K27me3 demethylase activity, is essential
for C. elegans development (Vandamme et al., 2012). Worms
lacking all three JmjD3 genes are viable and fertile and there is no
evidence for a major functional redundancy between UTX-1 and
the three JmjD3 proteins (Vandamme et al., 2012).
Drosophila contains a single Utx gene, also called dUtx (Smith et
al., 2008). Recent studies analysed the phenotype of Drosophila Utx
mutants containing a premature termination codon in the C-terminal
portion of the JmjC domain (Herz et al., 2010). A large proportion
of the animals homozygous for this allele died during the pupal
stages, but some were found to develop into adults that showed a
spectrum of phenotypes, including rough eyes and mortality shortly
after eclosion (Herz et al., 2010). Based on studies with this allele
in mosaic animals, it was proposed that Utx acts as a tumour
suppressor in Drosophila (Herz et al., 2010).
In this study, we generated a Drosophila Utx knockout allele
carrying a deletion of the catalytic JmjC domain. Our analyses of
Utx mutants provide no evidence for a tumour suppressor function
of Utx and show that the zygotic Utx product is dispensable for the
normal development of epidermal structures but is essential for adult
viability. However, we found that maternally deposited Utx protein
in the early embryo is crucial for the normal expression of multiple
HOX genes. This work establishes Utx as a trithorax group (trxG)
regulator that is specifically required early in embryogenesis to set
up long-term stable HOX gene expression patterns.
Fig. 1. Analysis of Utx protein in Utx mutants and requirement for
Utx in Drosophila development. (A) Domain architecture of the
Drosophila Utx protein showing the tetratricopeptide repeats (TPR) and
the catalytic JmjC domain. The lesions of the previously described Utx1
allele (Herz et al., 2010) and of the UtxΔ deletion allele are indicated; in
UtxΔ, a Ser503>stop mutation was introduced and a large portion of the
JmjC coding region was deleted. (B) Total extracts from imaginal disc and
CNS tissues from wild-type (wt, lane 1), homozygous Utx1 (lane 2) and
homozygous UtxΔ (lane 3) larvae probed with an antibody against
Utx420-633. Note the lack of the 145 and 80 kDa bands (arrowheads) in the
Utx1 and UtxΔ mutant extracts. Each lane contained the extract from ten
third instar larvae and non-specific cross-reacting bands detected by the
antibody provide an additional control for loading of comparable
amounts of extract. (C) Survival of wild type and Utx mutants of the
indicated genotypes to adults; Df Utx indicates Df(2L)BSC143 and mat+
zyg– indicates that these animals were obtained from Utx1 and UtxΔ
heterozygous mothers. mat– zyg– animals were obtained from mothers
with UtxΔ germline clones; they arrest development before the pupal
stage (no adults were obtained, asterisk) (see main text). For each
genotype, three independent batches with 100 first instar larvae each
were collected, transferred into vials and the number of eclosed adults
was determined. Error bars indicate s.d.
(Fig. 1A; supplementary material Fig. S1). Utx∆ is thus a
molecularly defined H3-K27 demethylase deficiency allele. We
generated extracts from wild-type larvae and from larvae that were
homozygous for Utx∆ or Utx1, a previously described point mutation
(Fig. 1A) (Herz et al., 2010), and probed them with antibodies that
had been raised against a central portion [anti-Utx420-633 (Tie et al.,
2012)] or the N-terminus [anti-dUtx1-153 (Herz et al., 2010), referred
to here as anti-Utx1-153] of the Utx protein. In wild-type extracts,
the anti-Utx420-633 antibody detected two bands with apparent
molecular weights of 145 and 80 kDa that were both absent in Utx∆
or Utx1 mutant extracts (Fig. 1B). This suggests that both the 145
and the 80 kDa proteins are Utx products. Although the 80 kDa
band appears more intense than the 145 kDa band and could thus
represent an alternate, shorter Utx product, it is also possible that the
80 kDa band represents a degradation product of the 145 kDa
The anti-Utx1-153 antibody detected the 145 kDa but not the 80
kDa band in wild-type extracts, suggesting that the 80 kDa Utx
product lacks the N-terminus (data not shown). The anti-Utx1-153
antibody also no longer detected the 145 kDa band in Utx∆ extracts,
but instead detected an extra band of ~55 kDa that is absent in wildtype extracts and is likely to correspond to the Utx1-502 protein
encoded by Utx∆ (data not shown). In summary, the molecularly
Development 140 (16)
defined deletion of the JmjC domain in Utx∆ and these western blot
analyses demonstrate that Utx∆ is a demethylase null mutation.
In a first set of experiments, we examined the phenotype of
Utx∆/Df(2L)BSC143 transheterozygotes that were derived from
females with a Utx∆ heterozygous germ line. Although these
mutants do not express wild-type Utx protein from their genome,
they still contain wild-type Utx product during the earliest stages
of development, deposited in the egg by the mother. We refer to
these as Utx∆ mat+ zyg– mutants to distinguish them from Utx∆ mat– zyg–
mutants that are derived from females with Utx∆ germ cells and
which therefore completely lack wild-type Utx protein (see below).
The majority of Utx∆ mat+ zyg– animals develop into adults that are
morphologically indistinguishable from wild-type flies, but die
within a day after eclosion from the pupal case (Fig. 1C). Previous
studies reported that animals homozygous for Utx1 only rarely
survive to adults and that surviving individuals show a rough eye
phenotype and die shortly after eclosion (Herz et al., 2010). We
found that Utx1/Utx1 homozygotes indeed only rarely survive to
adults (Fig. 1C) but that Utx1/Df(2L)BSC143 transheterozygotes
develop into adults at a frequency comparable to
Utx∆/Df(2L)BSC143 transheterozygotes or Utx∆ homozygotes and
that these animals show no detectable morphological defects
(Fig. 1C; data not shown). As in the case of Utx∆ adults,
Utx1/Df(2L)BSC143 transheterozygous adults also die shortly after
eclosion. We conclude that zygotic Utx function is not required for
the development of morphologically normal epidermal structures
but, for unknown reasons, it is essential for adult viability.
Global H3-K27me3 and H3-K27ac levels are
unaffected in Utx mutants
We next investigated how loss of Utx demethylase activity affects
the global levels of H3-K27me3. Previous studies reported that bulk
H3-K27me3 levels in Utx1 homozygous larvae or in Utx RNAitreated adults are increased compared with wild-type animals (Herz
et al., 2010; Tie et al., 2012) and that bulk levels of histone H3
acetylation at lysine 27 (H3-K27ac) are decreased (Tie et al., 2012).
We performed western blot analyses on serially diluted extracts
from Utx∆/Df(2L)BSC143 or Utx1/Df(2L)BSC143 larvae with antiH3-K27me3 and anti-H3-K27ac antibodies. We were unable to
detect a change in the bulk levels of these modifications in Utx
mutants compared with wild-type larvae (Fig. 2A). Probing the
same material with an antibody against H3-K4me1, we found a very
small but reproducible decrease in bulk H3-K4me1 levels in Utx
mutants (Fig. 2A), consistent with a previous report (Herz et al.,
2010). We also analysed H3-K27me3, H3-K27ac and H3-K4me1
levels by immunofluorescence labelling of imaginal wing discs with
clones of Utx∆ or Utx1 cells. We found that H3-K27me3 and H3K27ac, but also H3-K4me1, immunofluorescence signals in Utx∆
or Utx1 cells were comparable to those in neighbouring wild-type
cells in the same tissue (Fig. 2B; data not shown). We conclude that
lack of Utx has no major effect on global H3-K27me3 and H3K27ac levels but results in a very small reduction in global H3K4me1 levels.
Utx mutant cells proliferate like wild-type cells
Previous studies reported that Utx1 cell clones in imaginal discs
show a growth advantage relative to neighbouring wild-type cells
and proposed that Utx acts as a tumour suppressor (Herz et al.,
2010). We used the exact same experimental conditions as Herz and
co-workers (Herz et al., 2010) to analyse the size and growth of
Utx∆ or Utx1 cell clones in the eye-antenna imaginal disc but found
that both Utx∆ and Utx1 clones grow like control clones of wild-type
Fig. 2. Bulk H3-K27me3 and H3-K27ac levels are unchanged in Utx
mutants. (A) Western blots of serial dilutions (4:2:1) of total extracts from
imaginal disc and CNS tissues of wild-type (wt, lanes 1-3), Utx1/Df(2L)BSC143
(lanes 4-6) and UtxΔ/Df(2L)BSC143 (lanes 7-9) larvae, probed with antibodies
against H3-K27me3, H3-K27ac and H3-K4me1. In each case, the membrane
was simultaneously probed with an antibody against histone H4 to control
for extract loading and western blot processing but was exposed to film for
a shorter period of time in order not to saturate the H4 signal. Note that H3K27me3 and H3-K27ac levels are unchanged in Utx mutant extracts but that
H3-K4me1 levels are very slightly (less than one-third) decreased in the
mutants. (B) Wing imaginal discs with MARCM clones of UtxΔ homozygous
cells that are marked by the presence of GFP, stained with H3-K27me3 or H3K27ac antibodies and Hoechst (for DNA). Note that the H3-K27me3 and H3K27ac immunofluorescence signals in UtxΔ/UtxΔ clone cells are comparable
to those in the neighbouring UtxΔ/+ cells. Discs were analysed 96 hours after
clone induction.
cells that we induced as reference in a parallel experiment (Fig. 3).
Using the ey-flp driver to induce clones across the entire eyeantenna imaginal disc, we found that adults with Utx1 eyes show a
rough eye phenotype similar to that reported for surviving Utx1
homozygotes (Herz et al., 2010) (data not shown). Since
Utx1/Df(2L)BSC143 transheterozygotes and Utx∆ homozygotes do
not show this phenotype, it seems likely that this rough eye
phenotype is caused by a second site mutation on the 2L
chromosome arm carrying the Utx1 allele. In summary, these
analyses provide no evidence that Utx mutant cells would have a
growth advantage compared with wild-type cells.
Maternally deposited Utx is essential for stably
activated HOX gene expression
We next analysed the phenotype of mutants that lack both maternal
and zygotic Utx product. We generated Utx∆/Df(2L)BSC143 animals
from females with Utx∆ germ cells. These Utx∆ mat– zyg– animals
Fig. 3. Utx1 and UtxΔ clones do not show an overproliferation
phenotype. Eye-antenna imaginal discs with MARCM clones of Utx1 or
UtxΔ homozygous cells marked by the presence of GFP and stained with
Hoechst. As reference, clones of a wild-type 2L chromosome arm (wt)
were generated the same way and are also positively marked by GFP
(top). In all cases, discs were analysed 96 hours after clone induction. Note
that the clone sizes are comparable in all three genotypes and that the
clone cells populate a comparable area of disc tissue.
develop to the larval stages; 85% die before reaching the third larval
instar and the remaining larvae die during the third larval instar, with
only a very small fraction (0.6%) developing to form white prepupae,
which then also die (Fig. 1C). Thus, complete absence of Utx does not
permit animals to develop beyond the third larval instar or to undergo
metamorphosis, suggesting an essential function of maternally
supplied Utx products. Nevertheless, if Utx∆ oocytes (i.e. derived
from females with a Utx∆ germ line) are fertilised by wild-type sperm,
zygotic expression of Utx protein rescues these Utx∆ mat– zyg+ animals
into viable and fertile adults. The majority of such Utx∆ mat– zyg+ adults
show wild-type morphology but a substantial fraction shows
homeotic transformations that are reminiscent of trithorax (trx)
mutants (Ingham and Whittle, 1980) and are likely to be caused by a
reduction or loss of expression of HOX genes (see below).
Specifically, 30% of Utx∆ mat– zyg+ males (n=382) show a patchy loss
of pigmentation in the tergite of the fifth abdominal segment (A5),
which represents a transformation of the affected tissue into a more
anterior abdominal segment and is caused by loss of Abd-B
expression in A5 (Fig. 4A). At very low frequency (2.8%, n=758),
Utx∆ mat– zyg+ individuals also show transformation of parts of the
haltere into wing tissue (not shown), a homeotic transformation
caused by the loss of Ultrabithorax (Ubx) expression in this body
The trx-like phenotypes in Utx∆ mat– zyg+ adults prompted us to
analyse the expression of HOX genes in Utx∆ mat– zyg– animals.
Utx∆ mat– zyg– mutant embryos show a strong reduction of Abd-B
expression in parasegment (ps) 10 (Fig. 4B), from which the A5
segment of adults (Fig. 4A) is derived. Abd-B expression in the
Utx function in Drosophila
Development 140 (16)
Fig. 4. Trithorax-like homeotic transformations and loss of HOX gene
expression in UtxΔ mutants. (A) Portions of the dorsal abdomen of adult
males of the indicated genotype, showing the tergites of abdominal
segments A4, A5 and A6. Note the patchy loss of pigmentation in the
anterior part of A5 of the UtxΔ mat– zyg+ male (arrowheads), suggesting a
transformation of this tissue to A4 segment identity. (B) Ventral views of
stage 16 embryos stained with antibodies against the HOX proteins Ubx and
Abd-B. The UtxΔ mat– zyg– genotype refers to UtxΔ/Df(2L)BSC143 embryos
derived from females with a UtxΔ germ line. Ubx expression is
indistinguishable from wild type (wt). Abd-B expression is strongly reduced
in parasegment (ps) 10 (arrowhead) but appears largely undiminished in
more posterior parasegments; a vertical bar marks the anterior margin of the
normal Abd-B expression domain in ps 10 in the CNS. (C) Haltere imaginal
discs from third instar larvae stained with Ubx antibody and Hoechst.
Mutant genotypes are UtxΔ/Df(2L)BSC143 derived from a UtxΔ heterozygous
mother (UtxΔ mat+ zyg–, middle) and from a female with a UtxΔ germ line
(UtxΔ mat– zyg–, bottom). Note the complete loss of Ubx expression in a large
fraction of cells in the UtxΔ mat– zyg– disc (asterisk) and that Ubx expression in
the UtxΔ mat+ zyg– disc is indistinguishable from the wild type. The loss of Ubx
expression is not compartment specific and always occurs in a clone-like
pattern with large patches of Ubx-negative cells.
more posterior ps 11-14 appears largely undiminished with the
exception of occasionally reduced expression in a few cells in ps
11 (Fig. 4B). We were unable to detect a reduction of Ubx
expression in Utx∆ mat– zyg– embryos compared with wild-type
embryos (Fig. 4B).
We next analysed HOX gene expression in imaginal discs of
Utx∆ mat– zyg– larvae that survived to the third larval instar (see above).
Distinct temporal requirements for the trxG
regulators Utx, Trx and Ash1
The observation that Utx is required for the long-term expression of
multiple HOX genes classifies Utx as a trxG regulator (Kennison
and Tamkun, 1988; Kennison, 1995). However, the temporal
requirement for Utx during the Drosophila life cycle is very distinct
from that of other trxG proteins such as Trx and Ash1. Specifically,
maternally deposited Utx product is sufficient to permit Drosophila
to develop into adults with morphologically normal epidermal
structures (i.e. in Utx∆ mat+ zyg– animals). Maternal Utx product
becomes extensively diluted during embryonic and larval cell
divisions and Utx∆ mat+ zyg– third instar larvae indeed lack detectable
levels of wild-type Utx protein (Fig. 1B). For the regulation of HOX
gene expression – though not for viability of adults – Utx therefore
appears to be required only early in development. This stands in
clear contrast to the requirement for Trx and Ash1; the function of
these proteins is needed throughout development and removal of
either protein from wild-type cells during the larval stages results in
loss of HOX gene expression (Ingham, 1981; Klymenko and
Müller, 2004).
One possible explanation for the lack of a trxG phenotype in
animals lacking zygotic Utx protein (i.e. in Utx∆ mat+ zyg– mutants)
could be that Utx function during larval development is redundant
in the presence of Ash1 or Trx. We investigated this possibility as
follows. Clones of cells that are homozygous for the protein-null
mutation ash122 in haltere or third leg imaginal discs show loss of
Ubx expression in the majority of cells but a fraction of cells
In wild-type animals, Ubx is expressed in all cells of the haltere and
third leg discs, Abd-B is expressed in a characteristic pattern in the
genital disc, and Scr is expressed in all cells of the first leg disc
(Fig. 4C; data not shown). Utx∆ mat– zyg– mutant larvae show complete
loss of Ubx expression in a patchy pattern in haltere and third leg
discs (Fig. 4C). Even though Ubx protein is undetectable in a
substantial fraction of cells in these discs, its expression level in the
remaining cells in these tissues appears undiminished compared with
wild-type animals (Fig. 4C). The patchy nature of the Ubx-negative
tissue, as opposed to a salt-and-pepper distribution of Ubx-negative
and -positive cells across the tissue, suggests that the Ubx-negative
cells are of clonal origin, a notion that we have not been able to test.
This Ubx loss of expression phenotype was observed in all third instar
larvae analysed, but the fraction of cells that show complete loss of
expression varied between individuals. Abd-B protein expression in
the genital disc of Utx∆ mat– zyg– larvae appeared indistinguishable from
that of wild-type animals (not shown). It should be noted that the
genital disc represents the primordium for abdominal segment A8,
A9 and A10 structures and that loss of Abd-B expression in
Utx∆ mat– zyg– embryos was restricted to ps 10, which is the primordium
of abdominal segment A5 in adults (Fig. 4B). Similarly, the homeotic
transformations in Utx∆ mat– zyg+ adults were also limited to A5
(Fig. 4A). In Utx mutants, Abd-B expression is thus only affected in
a subset of cells of the Abd-B expression domain. Finally, we found
Scr protein expression in first leg discs of Utx∆ mat– zyg– larvae to be
indistinguishable from that of wild type (data not shown). We also
note that, in imaginal discs of Utx∆ mat+ zyg– animals, expression of all
three HOX genes (Ubx, Abd-B and Scr) was indistinguishable from
wild type, consistent with the lack of homeotic phenotypes in adults
of this genotype (Fig. 4C; data not shown). Taken together, these data
show that Utx function in the very early Drosophila embryo is
required for the stable expression of the HOX genes Ubx and Abd-B,
but that zygotic Utx function is dispensable for normal HOX gene
Utx function in Drosophila
dispensable for normal morphogenesis of epidermal structures,
Utx∆ mat+ zyg– adults nevertheless die shortly after eclosion from the
pupal case. It is possible that this lethality is caused by defective
morphogenesis of internal tissues or organs. Alternatively, Utx
might be needed for some other vital function in adult Drosophila.
Below, we discuss in turn the conclusions that can be drawn from
these results and consider possible mechanisms as to how Utx might
regulate HOX gene expression.
nevertheless maintains high or moderate levels of Ubx expression
(Fig. 5) (see Klymenko and Müller, 2004). This all-or-none loss of
expression phenotype is also observed in ash122 homozygotes, and
it correlates with the accumulation of H3-K27me3 at the Ubx
promoter and coding regions in haltere and third leg imaginal disc
cells (Papp and Müller, 2006). If zygotically expressed Utx protein
synergised with Ash1 in imaginal disc cells to maintain HOX gene
expression, one might expect a more extensive loss of Ubx
expression in clones of Utx∆; ash122 double-mutant cells. We
therefore induced clones of ash122 homozygous cells in Utx∆ mat+
animals (Fig. 5). However, we found that the fraction of cells
that maintain high levels of Ubx expression in these ash122 Utx∆
double-mutant clones was comparable to that in ash122 singlemutant clones (Fig. 5). Thus, even in a genetic background in which
another trxG regulator is removed, there is no evidence for a role of
zygotic Utx protein in HOX gene regulation.
In this study, we used a Utx allele with a deletion of the catalytic
domain to investigate the role of Utx and its H3-K27 demethylase
activity in Drosophila development. Analyses of animals that lack
maternal and zygotic Utx product uncovered that Utx protein is
crucial for the long-term stable expression of multiple HOX genes.
By contrast, animals that lack only zygotic expression of Utx
develop into adults with morphologically normal epidermal
structures, suggesting that zygotic Utx function is not needed for
HOX gene regulation. Moreover, in animals lacking maternally
deposited Utx protein, zygotic Utx product alone is unable to fully
rescue normal HOX gene expression and these animals show
homeotic transformations (i.e. in Utx∆ mat– zyg+ animals). Together,
these data suggest that Utx function is crucial for HOX gene
regulation right at the onset of zygotic transcription in the early
embryo. Even though zygotic Utx expression is apparently
Possible molecular mechanisms of HOX gene
regulation by Utx
We envisage two possible mechanisms of how Utx could function
to activate the expression of HOX genes, one of which depends on
the H3-K27me3 demethylase activity of Utx and another that acts
independently of this enzymatic activity.
A first scenario would be that H3-K27me3 demethylation by Utx
in the early embryo removes ‘ectopic’ H3-K27 trimethylation by
PRC2 at HOX genes in cells in which these genes need to be
expressed. According to this view, the loss of HOX gene expression
in Utx∆ mat– zyg– animals would be due to ectopic placement of H3K27me3 and, as a consequence, PcG silencing of HOX genes within
their normal expression domains. H3-K27me3 demethylation by
Utx would thus act to antagonise the establishment of PcG
repression. Recent studies reported the genome-wide binding profile
of Utx in Drosophila tissue culture cells and found that Utx binding
colocalises tightly with the binding of PcG protein complexes at
Polycomb response elements (PREs) of HOX genes (Tie et al.,
2012). This supports the idea that the function of Utx in HOX gene
Fig. 5. Lack of Utx function does not exacerbate loss of HOX gene
expression in ash1 mutants. Haltere imaginal discs from third instar
larvae with clones of ash122 homozygous cells were stained with Ubx
antibody and Hoechst. ash122 mutant cells are marked by the absence of
GFP and were induced in a wild-type genetic background (ash122, top) or
in the background of UtxΔ mat+ zyg– homozygous larvae (UtxΔ, ash122,
bottom). Discs were analysed 96 hours after clone induction. In each
sample, the boundary of one clone is outlined. Note that in both
genotypes a fraction of cells in the clone shows complete loss of Ubx
expression (open arrowheads), whereas other cells maintain high to
moderate levels of Ubx expression (white arrowheads).
The requirement for Utx function is more limited
than for PRC2
Considering that Utx is the only known H3-K27 demethylase in
Drosophila, it is interesting to compare the requirement for Utx with
that for PRC2 during Drosophila development. First, germ cells
with null mutations in different PRC2 subunits fail to develop
(Phillips and Shearn, 1990; Birve et al., 2001), but Utx∆ mutant
germ cells develop into oocytes that support embryonic
development (this study). PRC2 is thus essential for germ cell
development whereas Utx is not. Second, removal of PRC2 subunits
in somatic cells at any time point during development (e.g. in
imaginal disc cells in larvae) results in misexpression of PRC2
target genes and cell fate changes (Birve et al., 2001; Müller et al.,
2002), but animals lacking zygotic Utx expression develop into
adults with normal epidermal morphology. PRC2 is thus
continuously required during embryonic and larval development.
By contrast, Utx is crucial during embryogenesis and in adults but
development from the third larval instar onwards, through pupal
development and metamorphosis, appears to occur largely normally
in the absence of detectable Utx protein (Fig. 1B).
Taken together, this argues against a view that transcriptional
regulation of PRC2 target genes during development involves a
constant interplay between H3-K27 methylation and demethylation.
In this context, it is interesting to note that, in second instar larvae
that lack zygotic PRC2 function but had survived up to this stage
because of maternally supplied PRC2, H3-K27me3 levels are
comparable to those in wild-type larvae at the same stage (Nekrasov
et al., 2007). This suggests that H3-K27me3 that was generated by
maternally supplied PRC2 remains stable when the supply of
maternal PRC2 disappears and de novo deposition of this
modification ceases. This further supports the notion that H3K27me3 is a stable modification in Drosophila that is apparently
not subject to constant turnover.
chromatin is intimately linked to that of PRC2. Below, we discuss
the possible relationship between this proposed role of Utx in
antagonising H3-K27me3 deposition by PRC2 and the role of Ash1
and Trx in the same process.
As discussed in the Introduction, previous studies reported that
Utx protein, but not its H3-K27me3 demethylase activity, is
essential for normal C. elegans development (Vandamme et al.,
2012) and for the correct differentiation of murine ESCs in vitro
(Wang et al., 2012). An alternative scenario would thus be that
Drosophila Utx promotes HOX gene transcription by a
demethylase-independent mechanism. How could this work? As in
worms and mammals, Drosophila Utx is a component of an
MLL3/4-like complex that includes the H3-K4 methyltransferase
Trithorax-related (Trr) (Cho et al., 2007; Issaeva et al., 2007; Lee et
al., 2007; Patel et al., 2007; Mohan et al., 2011; Vandamme et al.,
2012). Recent studies in Drosophila proposed that Trr is required for
genome-wide H3-K4 monomethylation at enhancers and that H3K27me3 demethylation of enhancers by Trr-associated Utx would
be a general mechanism to convert inactive to active enhancers
(Herz et al., 2012). Although we have been unable to detect changes
in bulk H3-K27me3 and H3-K27ac levels in Utx mutants, we found
a slight decrease in bulk H3-K4me1 levels (Fig. 2A), consistent with
earlier studies (Herz et al., 2010). This decrease in H3-K4me1 is
not simply due to a reduction in Trr protein levels because these
were found to be undiminished after RNAi-mediated knockdown
of Utx (Herz et al., 2012). One possibility would thus be that Utx is
needed for H3-K4 monomethylation by Trr and thereby contributes
to the activation of HOX gene expression in the early embryo. trr
zygotic mutants die as embryos without any obvious trxG mutant
phenotypes (Sedkov et al., 1999), but the phenotype of embryos
lacking maternal and zygotic Trr protein is not known and so it is
currently unclear whether Trr plays a role in HOX gene regulation
in the early embryo. In the context of this scenario, we would
emphasize that Utx∆ mat– zyg– mutants develop to the larval stages
and, with some notable exceptions (i.e. the regulation of Abd-B
expression in ps 10 in the embryo), the enhancer-mediated
activation of genes required for embryonic patterning must therefore
by and large occur normally in the absence of Utx. Similarly,
Utx∆ mat+ zyg– larvae develop into morphologically normal adults and
the reduction of H3-K4me1 levels in these animals does not
therefore seem to compromise enhancer activity in any drastic
Relationship between Utx, Ash1 and Trx in
maintaining HOX gene expression
Utx, Ash1 and Trx are all required for the normal stable expression
of multiple HOX genes. Previous studies provided several
independent lines of genetic and biochemical evidence that Trx and
Ash1 keep HOX genes active by antagonising PRC2 activity. First,
HOX gene expression is lost in ash1 mutants but is restored in ash1
mutants that also lack E(z), the catalytic subunit of PRC2, suggesting
that Ash1 is not needed for HOX gene transcription but rather to
prevent PRC2 from shutting down HOX gene expression (Klymenko
and Müller, 2004). Second, chromatin immunoprecipitation studies of
the HOX gene Ubx in imaginal discs have shown that although PRC2
is also bound at Ubx in cells in which it is transcribed, Ash1 inhibits
deposition of H3-K27me3 at the promoter and coding region in these
cells (Papp and Müller, 2006). Third, on recombinant nucleosomes,
the histone modifications H3-K36me2/3 and H3-K4me3 that are
generated by Ash1 and Trx, respectively, strongly inhibit PRC2 from
methylating H3-K27 on the same histone tail (Schmitges et al., 2011;
Yuan et al., 2011).
Development 140 (16)
Here, we found that removal of Utx in imaginal disc cells has no
effect on HOX gene expression. Moreover, in ash1 mutant haltere
and third leg imaginal disc cells where PRC2 deposits faulty H3K27 trimethylation in the Ubx promoter and coding region (Papp
and Müller, 2006), and where Ubx expression is lost in many
although not all cells, removal of Utx does not exacerbate this loss
of Ubx expression (Fig. 5). This suggests that, at least in larvae, H3K27me3 demethylation is not crucial for antagonising the formation
of repressive H3-K27me3 chromatin on active HOX genes. During
larval development, H3-K4 and H3-K36 trimethylation by Trx,
Ash1 and possibly other H3-K4 and H3-K36 histone
methyltransferases therefore appears to be the predominant
mechanism that prevents HOX gene-bound PRC2 from depositing
H3-K27me3. This might, however, be different in the early embryo.
It is possible that during the establishment of HOX gene expression
domains at the blastoderm stage, H3-K4me3 and H3-K36me2/3
marks are not yet fully installed on HOX gene chromatin and that
it is during this critical time window that demethylation by Utx is
needed to remove faulty H3-K27me3 deposition from HOX genes
in cells in which they need to be expressed.
We thank A. Bergmann, P. Harte and Ali Shilatifard for the generous gift of fly
strains and antibodies; Andres Gaytan de Ayala and Tony Chen for help with
generating the UtxΔ disruption construct; and Sandra Müller for generation of
transgenic flies.
This work was supported by funds from the MPI of Biochemistry. Deposited in
PMC for immediate release.
Competing interests statement
The authors declare no competing financial interests.
Author contributions
O.C. and J.M. designed the experiments; O.C. carried out the experiments;
J.M. supervised the work and wrote the paper.
Supplementary material
Supplementary material available online at
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